Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/1aefd3b3f956d69c2b6dc48da48593/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/6b00395483f4902fc346076cb01524/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/6b00395483f4902fc346076cb01524/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/e2b0ae97d9758b9e85bf335abac811/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/e2b0ae97d9758b9e85bf335abac811/A673_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.Y9OTLpd8BA/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.Y9OTLpd8BA/cytoBand.txt Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed -parsing GTF file: /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.Y9OTLpd8BA/fi_workdir --reads "/tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' May 28 23:27:16 ..... started STAR run May 28 23:27:16 ..... loading genome May 28 23:29:18 ... generating Suffix Array index May 28 23:33:42 ... completed Suffix Array index May 28 23:33:42 ..... processing annotations GTF May 28 23:33:42 ..... inserting junctions into the genome indices May 28 23:34:45 ..... started mapping May 29 00:24:45 ..... finished mapping May 29 00:24:46 ..... started sorting BAM May 29 00:24:48 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam A673_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam Execution Time = 57.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.Y9OTLpd8BA/fi_workdir --reads "/tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups 00:25:13 : INFO : Done. Execution Time = 0.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/mark_dups_reads.index.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf -parsing /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] [1600000] [1610000] [1620000] [1630000] [1640000] [1650000] [1660000] [1670000] [1680000] [1690000] [1700000] [1710000] [1720000] [1730000] [1740000] [1750000] [1760000] [1770000] [1780000] [1790000] [1800000] [1810000] [1820000] [1830000] [1840000] [1850000] [1860000] [1870000] [1880000] [1890000] [1900000] [1910000] [1920000] [1930000] [1940000] [1950000] [1960000] [1970000] [1980000] [1990000] [2000000] [2010000] [2020000] [2030000] [2040000] [2050000] [2060000] [2070000] [2080000] [2090000] [2100000] [2110000] [2120000] [2130000] [2140000] [2150000] [2160000] [2170000] [2180000] [2190000] [2200000] [2210000] [2220000] [2230000] [2240000] [2250000] [2260000] [2270000] [2280000] [2290000] [2300000] [2310000] [2320000] [2330000] [2340000] [2350000] [2360000] [2370000] [2380000] [2390000] [2400000] [2410000] [2420000] [2430000] [2440000] [2450000] [2460000] [2470000] [2480000] [2490000] [2500000] [2510000] [2520000] [2530000] [2540000] [2550000] [2560000] [2570000] [2580000] [2590000] [2600000] [2610000] [2620000] [2630000] [2640000] [2650000] [2660000] [2670000] [2680000] [2690000] [2700000] [2710000] [2720000] [2730000] [2740000] [2750000] [2760000] [2770000] [2780000] [2790000] [2800000] [2810000] [2820000] [2830000] [2840000] [2850000] [2860000] [2870000] [2880000] [2890000] [2900000] [2910000] [2920000] [2930000] [2940000] [2950000] [2960000] [2970000] [2980000] [2990000] [3000000] [3010000] [3020000] [3030000] [3040000] [3050000] [3060000] [3070000] [3080000] [3090000] [3100000] [3110000] [3120000] [3130000] [3140000] [3150000] [3160000] [3170000] [3180000] [3190000] [3200000] [3210000] [3220000] [3230000] [3240000] [3250000] [3260000] [3270000] [3280000] [3290000] [3300000] [3310000] [3320000] [3330000] [3340000] [3350000] [3360000] [3370000] [3380000] [3390000] [3400000] [3410000] [3420000] [3430000] [3440000] [3450000] [3460000] [3470000] [3480000] [3490000] [3500000] [3510000] [3520000] [3530000] [3540000] [3550000] [3560000] [3570000] [3580000] [3590000] [3600000] [3610000] [3620000] [3630000] [3640000] [3650000] [3660000] [3670000] [3680000] [3690000] [3700000] [3710000] [3720000] [3730000] [3740000] [3750000] [3760000] [3770000] [3780000] [3790000] [3800000] [3810000] [3820000] [3830000] [3840000] [3850000] [3860000] [3870000] [3880000] [3890000] [3900000] [3910000] [3920000] [3930000] -done parsing /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12, 'small anchor length' => 221, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 9, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 111, ' ** passed ** ' => 35630, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 343, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 16, 'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 24, 'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 3, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1010, 'per_id < 96' => 24297, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1965, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 72, 'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 48, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 364, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12, 'num genes matched < 2' => 12, 'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 90, 'excessive soft clipping' => 31356, 'seq-similar region overlap' => 1155, 'low complexity anchor region' => 20, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 232, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 78, 'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 59, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 875, 'exons hit < 2' => 3, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 36 }; -writing fusion junction support info. Execution Time = 2.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] -fusion SPANNING read extraction for scaff: CPSF6--HOOK1 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: CYP7B1--LINC01414 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] [505000] [506000] [507000] [508000] [509000] [510000] [511000] [512000] [513000] [514000] [515000] [516000] [517000] [518000] [519000] [520000] [521000] [522000] [523000] [524000] [525000] [526000] [527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] [595000] [596000] [597000] [598000] [599000] [600000] [601000] [602000] [603000] [604000] [605000] [606000] [607000] [608000] [609000] [610000] [611000] [612000] [613000] [614000] [615000] [616000] [617000] [618000] [619000] [620000] [621000] [622000] [623000] [624000] [625000] [626000] [627000] [628000] [629000] [630000] [631000] [632000] [633000] [634000] [635000] [636000] [637000] [638000] [639000] [640000] [641000] [642000] [643000] [644000] [645000] [646000] [647000] [648000] [649000] [650000] [651000] [652000] [653000] [654000] [655000] [656000] [657000] [658000] [659000] [660000] [661000] [662000] [663000] [664000] [665000] [666000] [667000] [668000] [669000] [670000] [671000] [672000] [673000] [674000] [675000] [676000] [677000] [678000] [679000] [680000] [681000] [682000] [683000] [684000] [685000] [686000] [687000] [688000] [689000] [690000] [691000] [692000] [693000] [694000] [695000] [696000] [697000] [698000] [699000] [700000] [701000] [702000] [703000] [704000] [705000] [706000] [707000] [708000] [709000] [710000] [711000] [712000] [713000] [714000] [715000] [716000] [717000] [718000] [719000] [720000] [721000] [722000] [723000] [724000] [725000] [726000] [727000] [728000] [729000] [730000] [731000] [732000] [733000] [734000] [735000] [736000] [737000] [738000] [739000] [740000] [741000] [742000] [743000] [744000] [745000] [746000] [747000] [748000] [749000] [750000] [751000] [752000] [753000] [754000] [755000] [756000] [757000] [758000] [759000] [760000] [761000] [762000] [763000] [764000] [765000] [766000] [767000] [768000] [769000] [770000] [771000] [772000] [773000] [774000] [775000] [776000] [777000] [778000] [779000] [780000] [781000] [782000] [783000] [784000] [785000] [786000] [787000] [788000] [789000] [790000] [791000] [792000] [793000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: HIVEP3--AL158828.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: HIVEP3--AL353613.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] -fusion SPANNING read extraction for scaff: IGH-@-ext--SPG7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] -fusion SPANNING read extraction for scaff: IGH@-ext--SPG7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] -fusion SPANNING read extraction for scaff: RCN3--FCGRT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] -fusion SPANNING read extraction for scaff: SMURF2P1--SP2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: SPG7--PLSCR5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: SPG7--AC092957.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: SUCLA2--AL158828.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: SUCLA2--AL353613.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] -fusion SPANNING read extraction for scaff: SUPT20H--CHRDL2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: TMEM132B--TDG -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 223015, 'lacks exon overlap' => 19275 }; Execution Time = 5.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -16380.158685 EM: Round [1] log likelihood: -16362.765462 EM: Round [2] log likelihood: -16359.099171 EM: Round [3] log likelihood: -16356.435669 EM: Round [4] log likelihood: -16354.186683 EM: Round [5] log likelihood: -16352.229281 EM: Round [6] log likelihood: -16350.509491 EM: Round [7] log likelihood: -16348.990529 EM: Round [8] log likelihood: -16347.643454 EM: Round [9] log likelihood: -16346.444519 EM: Round [10] log likelihood: -16345.373926 EM: Round [11] log likelihood: -16344.415015 EM: Round [12] log likelihood: -16343.553668 EM: Round [13] log likelihood: -16342.777852 EM: Round [14] log likelihood: -16342.077255 EM: Round [15] log likelihood: -16341.443003 EM: Round [16] log likelihood: -16340.867425 EM: Round [17] log likelihood: -16340.343870 EM: Round [18] log likelihood: -16339.866547 EM: Round [19] log likelihood: -16339.430402 EM: Round [20] log likelihood: -16339.031012 EM: Round [21] log likelihood: -16338.664494 EM: Round [22] log likelihood: -16338.327434 EM: Round [23] log likelihood: -16338.016823 EM: Round [24] log likelihood: -16337.730000 EM: Round [25] log likelihood: -16337.464615 EM: Round [26] log likelihood: -16337.218579 EM: Round [27] log likelihood: -16336.990041 EM: Round [28] log likelihood: -16336.777351 EM: Round [29] log likelihood: -16336.579041 EM: Round [30] log likelihood: -16336.393799 EM: Round [31] log likelihood: -16336.220453 EM: Round [32] log likelihood: -16336.057954 EM: Round [33] log likelihood: -16335.905359 EM: Round [34] log likelihood: -16335.761825 EM: Round [35] log likelihood: -16335.626592 EM: Round [36] log likelihood: -16335.498976 EM: Round [37] log likelihood: -16335.378358 EM: Round [38] log likelihood: -16335.264183 EM: Round [39] log likelihood: -16335.155947 EM: Round [40] log likelihood: -16335.053193 EM: Round [41] log likelihood: -16334.955507 EM: Round [42] log likelihood: -16334.862514 EM: Round [43] log likelihood: -16334.773872 EM: Round [44] log likelihood: -16334.689270 EM: Round [45] log likelihood: -16334.608424 EM: Round [46] log likelihood: -16334.531076 EM: Round [47] log likelihood: -16334.456988 EM: Round [48] log likelihood: -16334.385945 EM: Round [49] log likelihood: -16334.317747 EM: Round [50] log likelihood: -16334.252212 EM: Round [51] log likelihood: -16334.189174 EM: Round [52] log likelihood: -16334.128476 EM: Round [53] log likelihood: -16334.069979 EM: Round [54] log likelihood: -16334.013551 EM: Round [55] log likelihood: -16333.959071 EM: Round [56] log likelihood: -16333.906427 EM: Round [57] log likelihood: -16333.855516 EM: Round [58] log likelihood: -16333.806242 EM: Round [59] log likelihood: -16333.758517 EM: Round [60] log likelihood: -16333.712257 EM: Round [61] log likelihood: -16333.667387 EM: Round [62] log likelihood: -16333.623834 EM: Round [63] log likelihood: -16333.581533 EM: Round [64] log likelihood: -16333.540421 EM: Round [65] log likelihood: -16333.500441 EM: Round [66] log likelihood: -16333.461538 EM: Round [67] log likelihood: -16333.423662 EM: Round [68] log likelihood: -16333.386765 EM: Round [69] log likelihood: -16333.350804 EM: Round [70] log likelihood: -16333.315737 EM: Round [71] log likelihood: -16333.281525 EM: Round [72] log likelihood: -16333.248132 EM: Round [73] log likelihood: -16333.215522 EM: Round [74] log likelihood: -16333.183664 EM: Round [75] log likelihood: -16333.152527 EM: Round [76] log likelihood: -16333.122083 EM: Round [77] log likelihood: -16333.092304 EM: Round [78] log likelihood: -16333.063165 EM: Round [79] log likelihood: -16333.034642 EM: Round [80] log likelihood: -16333.006712 EM: Round [81] log likelihood: -16332.979354 EM: Round [82] log likelihood: -16332.952547 EM: Round [83] log likelihood: -16332.926272 EM: Round [84] log likelihood: -16332.900510 EM: Round [85] log likelihood: -16332.875245 EM: Round [86] log likelihood: -16332.850459 EM: Round [87] log likelihood: -16332.826138 EM: Round [88] log likelihood: -16332.802266 EM: Round [89] log likelihood: -16332.778829 EM: Round [90] log likelihood: -16332.755814 EM: Round [91] log likelihood: -16332.733208 EM: Round [92] log likelihood: -16332.710999 EM: Round [93] log likelihood: -16332.689175 EM: Round [94] log likelihood: -16332.667725 EM: Round [95] log likelihood: -16332.646638 EM: Round [96] log likelihood: -16332.625905 EM: Round [97] log likelihood: -16332.605515 EM: Round [98] log likelihood: -16332.585460 EM: Round [99] log likelihood: -16332.565731 EM: Round [100] log likelihood: -16332.546318 EM: Round [101] log likelihood: -16332.527214 EM: Round [102] log likelihood: -16332.508412 EM: Round [103] log likelihood: -16332.489903 EM: Round [104] log likelihood: -16332.471681 EM: Round [105] log likelihood: -16332.453738 EM: Round [106] log likelihood: -16332.436068 EM: Round [107] log likelihood: -16332.418665 EM: Round [108] log likelihood: -16332.401522 EM: Round [109] log likelihood: -16332.384634 EM: Round [110] log likelihood: -16332.367995 EM: Round [111] log likelihood: -16332.351599 EM: Round [112] log likelihood: -16332.335441 EM: Round [113] log likelihood: -16332.319516 EM: Round [114] log likelihood: -16332.303819 EM: Round [115] log likelihood: -16332.288345 EM: Round [116] log likelihood: -16332.273090 EM: Round [117] log likelihood: -16332.258049 EM: Round [118] log likelihood: -16332.243218 EM: Round [119] log likelihood: -16332.228592 EM: Round [120] log likelihood: -16332.214169 EM: Round [121] log likelihood: -16332.199943 EM: Round [122] log likelihood: -16332.185911 EM: Round [123] log likelihood: -16332.172069 EM: Round [124] log likelihood: -16332.158414 EM: Round [125] log likelihood: -16332.144942 EM: Round [126] log likelihood: -16332.131650 EM: Round [127] log likelihood: -16332.118534 EM: Round [128] log likelihood: -16332.105592 EM: Round [129] log likelihood: -16332.092820 EM: Round [130] log likelihood: -16332.080216 EM: Round [131] log likelihood: -16332.067776 EM: Round [132] log likelihood: -16332.055497 EM: Round [133] log likelihood: -16332.043377 EM: Round [134] log likelihood: -16332.031414 EM: Round [135] log likelihood: -16332.019603 EM: Round [136] log likelihood: -16332.007944 EM: Round [137] log likelihood: -16331.996432 EM: Round [138] log likelihood: -16331.985067 EM: Round [139] log likelihood: -16331.973845 EM: Round [140] log likelihood: -16331.962764 EM: Round [141] log likelihood: -16331.951822 EM: Round [142] log likelihood: -16331.941017 EM: Round [143] log likelihood: -16331.930346 EM: Round [144] log likelihood: -16331.919808 EM: Round [145] log likelihood: -16331.909400 EM: Round [146] log likelihood: -16331.899120 EM: Round [147] log likelihood: -16331.888966 EM: Round [148] log likelihood: -16331.878937 EM: Round [149] log likelihood: -16331.869030 EM: Round [150] log likelihood: -16331.859244 EM: Round [151] log likelihood: -16331.849577 EM: Round [152] log likelihood: -16331.840026 EM: Round [153] log likelihood: -16331.830591 EM: Round [154] log likelihood: -16331.821270 EM: Round [155] log likelihood: -16331.812060 EM: Round [156] log likelihood: -16331.802961 EM: Round [157] log likelihood: -16331.793970 EM: Round [158] log likelihood: -16331.785086 EM: Round [159] log likelihood: -16331.776308 EM: Round [160] log likelihood: -16331.767633 EM: Round [161] log likelihood: -16331.759061 EM: Round [162] log likelihood: -16331.750591 EM: Round [163] log likelihood: -16331.742220 EM: Round [164] log likelihood: -16331.733947 EM: Round [165] log likelihood: -16331.725771 EM: Round [166] log likelihood: -16331.717690 EM: Round [167] log likelihood: -16331.709703 EM: Round [168] log likelihood: -16331.701810 EM: Round [169] log likelihood: -16331.694008 EM: Round [170] log likelihood: -16331.686296 EM: Round [171] log likelihood: -16331.678673 EM: Round [172] log likelihood: -16331.671139 EM: Round [173] log likelihood: -16331.663690 EM: Round [174] log likelihood: -16331.656328 EM: Round [175] log likelihood: -16331.649049 EM: Round [176] log likelihood: -16331.641854 EM: Round [177] log likelihood: -16331.634741 EM: Round [178] log likelihood: -16331.627710 EM: Round [179] log likelihood: -16331.620758 EM: Round [180] log likelihood: -16331.613884 EM: Round [181] log likelihood: -16331.607089 EM: Round [182] log likelihood: -16331.600371 EM: Round [183] log likelihood: -16331.593728 EM: Round [184] log likelihood: -16331.587160 EM: Round [185] log likelihood: -16331.580666 EM: Round [186] log likelihood: -16331.574245 EM: Round [187] log likelihood: -16331.567896 EM: Round [188] log likelihood: -16331.561618 EM: Round [189] log likelihood: -16331.555410 EM: Round [190] log likelihood: -16331.549271 EM: Round [191] log likelihood: -16331.543201 EM: Round [192] log likelihood: -16331.537198 EM: Round [193] log likelihood: -16331.531262 EM: Round [194] log likelihood: -16331.525391 EM: Round [195] log likelihood: -16331.519585 EM: Round [196] log likelihood: -16331.513844 EM: Round [197] log likelihood: -16331.508166 EM: Round [198] log likelihood: -16331.502550 EM: Round [199] log likelihood: -16331.496996 EM: Round [200] log likelihood: -16331.491503 EM: Round [201] log likelihood: -16331.486070 EM: Round [202] log likelihood: -16331.480697 EM: Round [203] log likelihood: -16331.475383 EM: Round [204] log likelihood: -16331.470126 EM: Round [205] log likelihood: -16331.464927 EM: Round [206] log likelihood: -16331.459784 EM: Round [207] log likelihood: -16331.454698 EM: Round [208] log likelihood: -16331.449666 EM: Round [209] log likelihood: -16331.444689 EM: Round [210] log likelihood: -16331.439766 EM: Round [211] log likelihood: -16331.434896 EM: Round [212] log likelihood: -16331.430079 EM: Round [213] log likelihood: -16331.425314 EM: Round [214] log likelihood: -16331.420600 EM: Round [215] log likelihood: -16331.415937 EM: Round [216] log likelihood: -16331.411324 EM: Round [217] log likelihood: -16331.406760 EM: Round [218] log likelihood: -16331.402246 EM: Round [219] log likelihood: -16331.397779 EM: Round [220] log likelihood: -16331.393361 EM: Round [221] log likelihood: -16331.388990 EM: Round [222] log likelihood: -16331.384665 EM: Round [223] log likelihood: -16331.380386 EM: Round [224] log likelihood: -16331.376153 EM: Round [225] log likelihood: -16331.371965 EM: Round [226] log likelihood: -16331.367822 EM: Round [227] log likelihood: -16331.363722 EM: Round [228] log likelihood: -16331.359666 EM: Round [229] log likelihood: -16331.355653 EM: Round [230] log likelihood: -16331.351682 EM: Round [231] log likelihood: -16331.347753 EM: Round [232] log likelihood: -16331.343866 EM: Round [233] log likelihood: -16331.340020 EM: Round [234] log likelihood: -16331.336214 EM: Round [235] log likelihood: -16331.332448 EM: Round [236] log likelihood: -16331.328722 EM: Round [237] log likelihood: -16331.325035 EM: Round [238] log likelihood: -16331.321387 EM: Round [239] log likelihood: -16331.317777 EM: Round [240] log likelihood: -16331.314204 EM: Round [241] log likelihood: -16331.310669 EM: Round [242] log likelihood: -16331.307171 EM: Round [243] log likelihood: -16331.303710 EM: Round [244] log likelihood: -16331.300285 EM: Round [245] log likelihood: -16331.296895 EM: Round [246] log likelihood: -16331.293541 EM: Round [247] log likelihood: -16331.290221 EM: Round [248] log likelihood: -16331.286936 EM: Round [249] log likelihood: -16331.283686 EM: Round [250] log likelihood: -16331.280468 EM: Round [251] log likelihood: -16331.277285 EM: Round [252] log likelihood: -16331.274134 EM: Round [253] log likelihood: -16331.271016 EM: Round [254] log likelihood: -16331.267930 EM: Round [255] log likelihood: -16331.264876 EM: Round [256] log likelihood: -16331.261853 EM: Round [257] log likelihood: -16331.258862 EM: Round [258] log likelihood: -16331.255902 EM: Round [259] log likelihood: -16331.252972 EM: Round [260] log likelihood: -16331.250072 EM: Round [261] log likelihood: -16331.247202 EM: Round [262] log likelihood: -16331.244362 EM: Round [263] log likelihood: -16331.241550 EM: Round [264] log likelihood: -16331.238768 EM: Round [265] log likelihood: -16331.236014 EM: Round [266] log likelihood: -16331.233288 EM: Round [267] log likelihood: -16331.230590 EM: Round [268] log likelihood: -16331.227920 EM: Round [269] log likelihood: -16331.225277 EM: Round [270] log likelihood: -16331.222661 EM: Round [271] log likelihood: -16331.220072 EM: Round [272] log likelihood: -16331.217509 EM: Round [273] log likelihood: -16331.214973 EM: Round [274] log likelihood: -16331.212462 EM: Round [275] log likelihood: -16331.209977 EM: Round [276] log likelihood: -16331.207517 EM: Round [277] log likelihood: -16331.205082 EM: Round [278] log likelihood: -16331.202671 EM: Round [279] log likelihood: -16331.200286 EM: Round [280] log likelihood: -16331.197924 EM: Round [281] log likelihood: -16331.195587 EM: Round [282] log likelihood: -16331.193273 EM: Round [283] log likelihood: -16331.190982 EM: Round [284] log likelihood: -16331.188715 EM: Round [285] log likelihood: -16331.186471 EM: Round [286] log likelihood: -16331.184249 EM: Round [287] log likelihood: -16331.182050 EM: Round [288] log likelihood: -16331.179873 EM: Round [289] log likelihood: -16331.177718 EM: Round [290] log likelihood: -16331.175585 EM: Round [291] log likelihood: -16331.173473 EM: Round [292] log likelihood: -16331.171382 EM: Round [293] log likelihood: -16331.169313 EM: Round [294] log likelihood: -16331.167264 EM: Round [295] log likelihood: -16331.165236 EM: Round [296] log likelihood: -16331.163229 EM: Round [297] log likelihood: -16331.161241 EM: Round [298] log likelihood: -16331.159274 EM: Round [299] log likelihood: -16331.157326 EM: Round [300] log likelihood: -16331.155398 EM: Round [301] log likelihood: -16331.153489 EM: Round [302] log likelihood: -16331.151599 EM: Round [303] log likelihood: -16331.149728 EM: Round [304] log likelihood: -16331.147876 EM: Round [305] log likelihood: -16331.146042 EM: Round [306] log likelihood: -16331.144227 EM: Round [307] log likelihood: -16331.142430 EM: Round [308] log likelihood: -16331.140651 EM: Round [309] log likelihood: -16331.138889 EM: Round [310] log likelihood: -16331.137146 EM: Round [311] log likelihood: -16331.135419 EM: Round [312] log likelihood: -16331.133710 EM: Round [313] log likelihood: -16331.132018 EM: Round [314] log likelihood: -16331.130343 EM: Round [315] log likelihood: -16331.128684 EM: Round [316] log likelihood: -16331.127042 EM: Round [317] log likelihood: -16331.125416 EM: Round [318] log likelihood: -16331.123806 EM: Round [319] log likelihood: -16331.122213 EM: Round [320] log likelihood: -16331.120635 EM: Round [321] log likelihood: -16331.119073 EM: Round [322] log likelihood: -16331.117526 EM: Round [323] log likelihood: -16331.115995 EM: Round [324] log likelihood: -16331.114479 EM: Round [325] log likelihood: -16331.112978 EM: Round [326] log likelihood: -16331.111492 EM: Round [327] log likelihood: -16331.110020 EM: Round [328] log likelihood: -16331.108563 EM: Round [329] log likelihood: -16331.107121 EM: Round [330] log likelihood: -16331.105693 EM: Round [331] log likelihood: -16331.104278 EM: Round [332] log likelihood: -16331.102878 EM: Round [333] log likelihood: -16331.101492 EM: Round [334] log likelihood: -16331.100120 EM: Round [335] log likelihood: -16331.098760 EM: Round [336] log likelihood: -16331.097415 EM: Round [337] log likelihood: -16331.096083 EM: Round [338] log likelihood: -16331.094763 EM: Round [339] log likelihood: -16331.093457 EM: Round [340] log likelihood: -16331.092164 EM: Round [341] log likelihood: -16331.090883 EM: Round [342] log likelihood: -16331.089615 EM: Round [343] log likelihood: -16331.088360 EM: Round [344] log likelihood: -16331.087117 EM: Round [345] log likelihood: -16331.085886 EM: Round [346] log likelihood: -16331.084667 EM: Round [347] log likelihood: -16331.083460 EM: Round [348] log likelihood: -16331.082265 EM: Round [349] log likelihood: -16331.081082 EM: Round [350] log likelihood: -16331.079911 EM: Round [351] log likelihood: -16331.078750 EM: Round [352] log likelihood: -16331.077602 EM: Round [353] log likelihood: -16331.076464 EM: Round [354] log likelihood: -16331.075338 EM: Round [355] log likelihood: -16331.074223 EM: Round [356] log likelihood: -16331.073119 EM: Round [357] log likelihood: -16331.072025 EM: Round [358] log likelihood: -16331.070942 EM: Round [359] log likelihood: -16331.069870 EM: Round [360] log likelihood: -16331.068809 EM: Round [361] log likelihood: -16331.067757 EM: Round [362] log likelihood: -16331.066716 EM: Round [363] log likelihood: -16331.065686 EM: Round [364] log likelihood: -16331.064665 EM: Round [365] log likelihood: -16331.063654 EM: Round [366] log likelihood: -16331.062653 EM: Round [367] log likelihood: -16331.061662 EM: Round [368] log likelihood: -16331.060681 EM: Round [369] log likelihood: -16331.059709 EM: Round [370] log likelihood: -16331.058747 EM: Round [371] log likelihood: -16331.057794 EM: Round [372] log likelihood: -16331.056850 EM: Round [373] log likelihood: -16331.055916 EM: Round [374] log likelihood: -16331.054990 EM: Round [375] log likelihood: -16331.054074 EM: Round [376] log likelihood: -16331.053167 EM: Round [377] log likelihood: -16331.052268 EM: Round [378] log likelihood: -16331.051378 EM: Round [379] log likelihood: -16331.050497 EM: Round [380] log likelihood: -16331.049625 EM: Round [381] log likelihood: -16331.048761 EM: Round [382] log likelihood: -16331.047905 EM: Round [383] log likelihood: -16331.047058 EM: Round [384] log likelihood: -16331.046219 EM: Round [385] log likelihood: -16331.045388 EM: Round [386] log likelihood: -16331.044565 EM: Round [387] log likelihood: -16331.043750 EM: Round [388] log likelihood: -16331.042943 EM: Round [389] log likelihood: -16331.042144 EM: Round [390] log likelihood: -16331.041353 EM: Round [391] log likelihood: -16331.040569 EM: Round [392] log likelihood: -16331.039793 EM: Round [393] log likelihood: -16331.039025 EM: Round [394] log likelihood: -16331.038264 EM: Round [395] log likelihood: -16331.037510 EM: Round [396] log likelihood: -16331.036764 EM: Round [397] log likelihood: -16331.036025 EM: Round [398] log likelihood: -16331.035293 EM: Round [399] log likelihood: -16331.034568 EM: Round [400] log likelihood: -16331.033850 EM: Round [401] log likelihood: -16331.033139 EM: Round [402] log likelihood: -16331.032435 EM: Round [403] log likelihood: -16331.031738 EM: Round [404] log likelihood: -16331.031048 EM: Round [405] log likelihood: -16331.030364 EM: Round [406] log likelihood: -16331.029687 EM: Round [407] log likelihood: -16331.029017 EM: Round [408] log likelihood: -16331.028352 EM: Round [409] log likelihood: -16331.027695 EM: Round [410] log likelihood: -16331.027044 EM: Round [411] log likelihood: -16331.026399 EM: Round [412] log likelihood: -16331.025760 EM: Round [413] log likelihood: -16331.025127 EM: Round [414] log likelihood: -16331.024501 EM: Round [415] log likelihood: -16331.023880 EM: Round [416] log likelihood: -16331.023266 EM: Round [417] log likelihood: -16331.022658 EM: Round [418] log likelihood: -16331.022055 EM: Round [419] log likelihood: -16331.021458 EM: Round [420] log likelihood: -16331.020867 EM: Round [421] log likelihood: -16331.020282 EM: Round [422] log likelihood: -16331.019702 EM: Round [423] log likelihood: -16331.019128 EM: Round [424] log likelihood: -16331.018560 EM: Round [425] log likelihood: -16331.017997 EM: Round [426] log likelihood: -16331.017439 EM: Round [427] log likelihood: -16331.016887 EM: Round [428] log likelihood: -16331.016340 EM: Round [429] log likelihood: -16331.015798 EM: Round [430] log likelihood: -16331.015262 EM: Round [431] log likelihood: -16331.014731 EM: Round [432] log likelihood: -16331.014204 EM: Round [433] log likelihood: -16331.013683 EM: Round [434] log likelihood: -16331.013167 EM: Round [435] log likelihood: -16331.012656 EM: Round [436] log likelihood: -16331.012150 EM: Round [437] log likelihood: -16331.011649 EM: Round [438] log likelihood: -16331.011152 EM: Round [439] log likelihood: -16331.010661 EM: Round [440] log likelihood: -16331.010174 EM: Round [441] log likelihood: -16331.009692 EM: Round [442] log likelihood: -16331.009214 EM: Round [443] log likelihood: -16331.008741 EM: Round [444] log likelihood: -16331.008272 EM: Round [445] log likelihood: -16331.007808 EM: Round [446] log likelihood: -16331.007349 EM: Round [447] log likelihood: -16331.006894 EM: Round [448] log likelihood: -16331.006443 EM: Round [449] log likelihood: -16331.005997 EM: Round [450] log likelihood: -16331.005555 EM: Round [451] log likelihood: -16331.005117 EM: Round [452] log likelihood: -16331.004683 EM: Round [453] log likelihood: -16331.004253 EM: Round [454] log likelihood: -16331.003828 EM: Round [455] log likelihood: -16331.003407 EM: Round [456] log likelihood: -16331.002990 EM: Round [457] log likelihood: -16331.002576 EM: Round [458] log likelihood: -16331.002167 EM: Round [459] log likelihood: -16331.001762 EM: Round [460] log likelihood: -16331.001360 EM: Round [461] log likelihood: -16331.000963 EM: Round [462] log likelihood: -16331.000569 EM: Round [463] log likelihood: -16331.000179 EM: Round [464] log likelihood: -16330.999793 EM: Round [465] log likelihood: -16330.999410 EM: Round [466] log likelihood: -16330.999031 EM: Round [467] log likelihood: -16330.998656 EM: Round [468] log likelihood: -16330.998284 EM: Round [469] log likelihood: -16330.997916 EM: Round [470] log likelihood: -16330.997551 EM: Round [471] log likelihood: -16330.997190 EM: Round [472] log likelihood: -16330.996833 EM: Round [473] log likelihood: -16330.996479 EM: Round [474] log likelihood: -16330.996128 EM: Round [475] log likelihood: -16330.995780 EM: Round [476] log likelihood: -16330.995436 EM: Round [477] log likelihood: -16330.995095 EM: Round [478] log likelihood: -16330.994758 EM: Round [479] log likelihood: -16330.994423 EM: Round [480] log likelihood: -16330.994092 EM: Round [481] log likelihood: -16330.993764 EM: Round [482] log likelihood: -16330.993439 EM: Round [483] log likelihood: -16330.993118 EM: Round [484] log likelihood: -16330.992799 EM: Round [485] log likelihood: -16330.992483 EM: Round [486] log likelihood: -16330.992171 EM: Round [487] log likelihood: -16330.991861 EM: Round [488] log likelihood: -16330.991555 EM: Round [489] log likelihood: -16330.991251 EM: Round [490] log likelihood: -16330.990950 EM: Round [491] log likelihood: -16330.990652 EM: Round [492] log likelihood: -16330.990357 EM: Round [493] log likelihood: -16330.990065 EM: Round [494] log likelihood: -16330.989775 EM: Round [495] log likelihood: -16330.989489 EM: Round [496] log likelihood: -16330.989205 EM: Round [497] log likelihood: -16330.988923 EM: Round [498] log likelihood: -16330.988645 EM: Round [499] log likelihood: -16330.988369 EM: Round [500] log likelihood: -16330.988096 EM: Round [501] log likelihood: -16330.987825 EM: Round [502] log likelihood: -16330.987557 EM: Round [503] log likelihood: -16330.987291 EM: Round [504] log likelihood: -16330.987028 EM: Round [505] log likelihood: -16330.986768 EM: Round [506] log likelihood: -16330.986510 EM: Round [507] log likelihood: -16330.986254 EM: Round [508] log likelihood: -16330.986001 EM: Round [509] log likelihood: -16330.985751 EM: Round [510] log likelihood: -16330.985502 EM: Round [511] log likelihood: -16330.985256 EM: Round [512] log likelihood: -16330.985013 EM: Round [513] log likelihood: -16330.984772 EM: Round [514] log likelihood: -16330.984533 EM: Round [515] log likelihood: -16330.984296 EM: Round [516] log likelihood: -16330.984062 EM: Round [517] log likelihood: -16330.983829 EM: Round [518] log likelihood: -16330.983599 EM: Round [519] log likelihood: -16330.983372 EM: Round [520] log likelihood: -16330.983146 EM: Round [521] log likelihood: -16330.982923 EM: Round [522] log likelihood: -16330.982701 EM: Round [523] log likelihood: -16330.982482 EM: Round [524] log likelihood: -16330.982265 EM: Round [525] log likelihood: -16330.982050 EM: Round [526] log likelihood: -16330.981837 EM: Round [527] log likelihood: -16330.981626 EM: Round [528] log likelihood: -16330.981417 EM: Round [529] log likelihood: -16330.981210 EM: Round [530] log likelihood: -16330.981005 EM: Round [531] log likelihood: -16330.980802 EM: Round [532] log likelihood: -16330.980601 EM: Round [533] log likelihood: -16330.980401 EM: Round [534] log likelihood: -16330.980204 EM: Round [535] log likelihood: -16330.980009 EM: Round [536] log likelihood: -16330.979815 EM: Round [537] log likelihood: -16330.979623 EM: Round [538] log likelihood: -16330.979433 EM: Round [539] log likelihood: -16330.979245 EM: Round [540] log likelihood: -16330.979059 EM: Round [541] log likelihood: -16330.978874 EM: Round [542] log likelihood: -16330.978692 EM: Round [543] log likelihood: -16330.978511 EM: Round [544] log likelihood: -16330.978331 EM: Round [545] log likelihood: -16330.978154 EM: Round [546] log likelihood: -16330.977978 EM: Round [547] log likelihood: -16330.977803 EM: Round [548] log likelihood: -16330.977631 EM: Round [549] log likelihood: -16330.977460 EM: Round [550] log likelihood: -16330.977290 EM: Round [551] log likelihood: -16330.977123 EM: Round [552] log likelihood: -16330.976957 EM: Round [553] log likelihood: -16330.976792 EM: Round [554] log likelihood: -16330.976629 EM: Round [555] log likelihood: -16330.976467 EM: Round [556] log likelihood: -16330.976308 EM: Round [557] log likelihood: -16330.976149 EM: Round [558] log likelihood: -16330.975992 EM: Round [559] log likelihood: -16330.975837 EM: Round [560] log likelihood: -16330.975683 EM: Round [561] log likelihood: -16330.975530 EM: Round [562] log likelihood: -16330.975379 EM: Round [563] log likelihood: -16330.975230 EM: Round [564] log likelihood: -16330.975082 EM: Round [565] log likelihood: -16330.974935 EM: Round [566] log likelihood: -16330.974789 EM: Round [567] log likelihood: -16330.974645 EM: Round [568] log likelihood: -16330.974503 EM: Round [569] log likelihood: -16330.974362 EM: Round [570] log likelihood: -16330.974222 EM: Round [571] log likelihood: -16330.974083 EM: Round [572] log likelihood: -16330.973946 EM: Round [573] log likelihood: -16330.973810 EM: Round [574] log likelihood: -16330.973675 EM: Round [575] log likelihood: -16330.973542 EM: Round [576] log likelihood: -16330.973409 EM: Round [577] log likelihood: -16330.973278 EM: Round [578] log likelihood: -16330.973149 EM: Round [579] log likelihood: -16330.973020 EM: Round [580] log likelihood: -16330.972893 EM: Round [581] log likelihood: -16330.972767 EM: Round [582] log likelihood: -16330.972642 EM: Round [583] log likelihood: -16330.972519 EM: Round [584] log likelihood: -16330.972396 EM: Round [585] log likelihood: -16330.972275 EM: Round [586] log likelihood: -16330.972155 EM: Round [587] log likelihood: -16330.972036 EM: Round [588] log likelihood: -16330.971918 EM: Round [589] log likelihood: -16330.971801 EM: Round [590] log likelihood: -16330.971685 EM: Round [591] log likelihood: -16330.971571 EM: Round [592] log likelihood: -16330.971457 EM: Round [593] log likelihood: -16330.971345 EM: Round [594] log likelihood: -16330.971233 EM: Round [595] log likelihood: -16330.971123 EM: Round [596] log likelihood: -16330.971014 EM: Round [597] log likelihood: -16330.970906 EM: Round [598] log likelihood: -16330.970798 EM: Round [599] log likelihood: -16330.970692 EM: Round [600] log likelihood: -16330.970587 EM: Round [601] log likelihood: -16330.970483 EM: Round [602] log likelihood: -16330.970380 EM: Round [603] log likelihood: -16330.970277 EM: Round [604] log likelihood: -16330.970176 EM: Round [605] log likelihood: -16330.970076 EM: Round [606] log likelihood: -16330.969976 EM: Stopping iterations at round 606 due to insufficient improvement in likelihood. Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/init_EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_extract_junc_reads.ok Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam" Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam || : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_sam_frag_coordss.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_pfam_bed.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/prep_igv_seqsim_bed.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Y9OTLpd8BA/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir -done, see /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -10339.490464 EM: Round [1] log likelihood: -10336.729600 EM: Round [2] log likelihood: -10336.729443 EM: Round [3] log likelihood: -10336.729442 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 295019057 Execution Time = 5.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.Y9OTLpd8BA/fi_workdir/microH.dat Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.Y9OTLpd8BA/fi_workdir/microH.dat Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Y9OTLpd8BA/fi_workdir/microH.dat /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Y9OTLpd8BA/fi_workdir/microH.dat /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Y9OTLpd8BA --json_outfile /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Y9OTLpd8BA --json_outfile /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1 Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/create_fi_igvjs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000253554.7] WARNING, no entry stored in dbm for [ENSG00000253554.7] WARNING, no entry stored in dbm for [ENSG00000232211.1] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Y9OTLpd8BA/ctat_genome_lib_build_dir > /tmp/nxf.Y9OTLpd8BA/A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.Y9OTLpd8BA/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory